AUN's governance structure stems from its American liberal arts heritage with the incorporation of distinctive Nigerian academic traditions tailored to the University’s specific philosophies.

The Chief Executive Officer of AUN is the President (Vice-Chancellor) who oversees the day-to-day management of the University. The President is assisted by the Provost (VP, Academics) and four other Vice Presidents - Campus Life & Dean of Student Affairs, Administration, Finance, and Safety & Security. The Registrar, who is also the VP for Administration, maintains the integrity of AUN’s academic database and provides administrative support to the University community.

Each of the University's Schools is led by a Dean who heads individual academic divisions.

The University Librarian is the custodian of AUN’s famed E-Library and expansive digital repository. Other officers of the University include Assistant Vice-Presidents, Directors, and line managers.